In Human Curiosity, it's theorized that the frozen nations are experiencing this, leading to Liechtenstein wanting to speak to Switzerland's body. Subverted in that when France recovers from having been frozen, he could not remember any of that time.
The people whose minds Kodachi Kuno of Divine Blood devours in order to take over their body as part of her collective are eventually shown as having fragmented pieces of their mental identity remaining in her collective mind as well as their entire souls enslaved to her will. When she manifests in a mindscape shortly before finally being exterminated, the mouths of the multitude of people she'd devoured are shown to be either gagged, sewn shut with needle and thread, ripped out or simply not there.
In Waking Nightmares, Celestia does this to the Zompony Grey Hoof. Not only was he imprisoned in the ruins of his home, Sunnytown, but a fear spell was placed on the land, one that causes all forms of life (including plant life), to flee in fear and become too afraid to approach. In addition to this, the town itself was shifted into a pocket dimension, and he was rendered unable to go insane. He's cursed to be alone forever, with no escape...
In the Horseshoes and Hand Grenades story, A Month of Sundays, Quetzalcoatl states that he was trapped underneath the remains of an ancient Aztec Temple for 500 years, screaming and begging for someone to help him.
In the series Lex Luthor Triumphant, Lex Luthor traps Superman, keeps him powerless with a combination of red sun rays and brain surgery. He develops an interface that allows him to control Superman's body and has him kill Lois Lane, after she finds out he captured, lobotomized, skinned Superman, and that selling his eye, skin, teeth, and fingernails has made Luthor even richer than before. So far, we haven't seen what happens in Superman's mind, but he's been depowered for almost the entire run. It's currently on chapter 5.
In the Teen Titans Saga, this is Veneficus' ultimate fate, as he is trapped in the void between dimensions with no means of escape. And since demons appear to be immortal barring being killed by someone else...
In Need for Control, Hojo had put Vincent through this as a method of torture that left him unable to function as a 'free' human being:
Vincent: "After my arm was removed, I was rendered unconscious again. When I awoke, I had no idea where I was. I found myself in the dark, unable to move. I couldn’t feel my body or hear anything. Even the air around me seemed to lack any type of smell whatsoever. At first, I found this to be a relief, thinking that if nothing else, that I wasn’t being tortured. However, that complete lack of external stimulation began to do something to me. Time seemed to have stopped, and I had no idea of how long I had been in there. I began to wonder if I was even alive… Not being able to feel, see, or hear anything does something to you after a time. I began to long for the torture. At least when that had been happening to me, I knew that I was alive."
However, that's not even the worst of it, as it's stated that all the time that Vincent was in the coffin before you find him? He's in that state. Twenty-seven to thirty years of it.
Vincent: "He put me back in the dark…I never even knew what it was that I’d done wrong… He just put me back in the dark and forgot about me… Twenty-seven years, Cid… I was in there for as long as I had been alive before Hojo had put me in there…"
In The Prince of Gryffindor Harry turned Voldemort into a sort of jellylike goo and trapped him in an unbreakable, unopenable jar while his mind was being tormented by an illusion of everyone and everything he'd killed/destroyed or ordered to be killed/destroyed.
At the end of Night of the Mannequins, Gaz is turned into a store mannequin after sneaking into the mall at night to be first in line for the new Game Slave 3. Worse still, she's put in a display window directly across from the store selling them, and it's strongly implied she's still aware.
Link Sr was sealed alone in the Fierce Deity mask for almost a century. He describes the ordeal as "goddamn annoying". Subverted by the fact that he canand does free himself without help, it just takes time.
Magi is considerably less fortunate. As punishment for ordering Link's people and family murdered just to get to him, he is chained in a Sealed Room in the Middle of Nowhere for roughly a decade while insects devour his honey-covered, disembodied heart over and over again.
The goddesses are implied to suffer this after Link awakens as the God of Fear and chains them to Fate and Destiny's former throne, but no details are given.
Link himself suffers this during his four seven-year naps when the goddesses see fit to send his mind through the Ocarina of Time adventure "about 3,500 times give or take a few hundred, each year, and in each timeline" for a total of 98,000 times over 28 years all for the purpose of refining his instincts to create as powerful a warrior as possible. They even had to tinker with his mind by building a "wall" around those instincts to contain them.
In one alternate ending to the infamous fanfic Cupcakes Pinkie Pie, unable to cope with the guilt of what she did under the influence of a Parasprite, voluntarily submitted herself to this via Taken for Granite.
Nihilus in turn does this to Rainbow Dash, subjecting her to a Mind Rape spell called the Insanity, which changes her into an insane, nigh-amnesiac berserker who serves as Nihilus' Dragon, with Dash stuck inside and tortured if she tries to fight back.
A flashback shows Titan apparently subjecting Discord to this (we only get vague details about it) after Discord caused the death of Titan's son. It's strongly implied that Celestia and Luna's defeat of Titan is what allowed Discord to escape. Though to be fair, Discord is considered the Lesser of Two Evils between him and Titan to the point the heroes actually free him to form an Enemy Mine against Titan.
In the Pony POV Series, it's shown that Dinky's fate in the Bad Future was to be turned into a filly-shaped muffin. When she's restored by the Elements of Harmony a thousand years later, it's revealed that she was completely aware of everything the entire time.
Also in the Bad Future, it turns out this was Fluttershy's fate as well. Fluttercruel, like in the main timeline, is a separate entity from Fluttershy who was granted control of their body. Unlike in the main POV verse, however, Dark World Fluttercruel remained in control and was raised by Discord instead of Fluttershy, becoming an even bigger monster than him, while Fluttershy was forced to watch all the horrible things she did. And on top of that, it turns out Fluttercruel liked to torture Fluttershy in their mindscape for fun. Fortunately, Cadence's spirit eventually managed to save Fluttershy's soul, though only after five hundred years of all this.
Turns out, even Discord himself was subjected to this in Dark World. Nightmare Paradox has kept him trapped in a "Groundhog Day" Loop that always ends in the deaths of his daughter and himself for somewhere in the equivalent of a few hundred million years. It's so bad that when he gets Dragged Off to Hell and horribly killed by his family for his crimes over a billion times, he doesn't mind in the least, as it's relaxing compared to what Paradox put him through.
Sweetheart's little sister Cream ended up suffering this in Sweetheart's 7 Dreams/Nightmares story. The shock from the explosion that destroyed G2 society ended up "locking her in", meaning her body was paralyzed to the point she couldn't even speak (worse, this is a real condition), but she was completely aware and conscious of everything. Including being dragged off and torn apart by mutants created by the explosion, taking this trope literally in that she literally couldn't scream. Worse in that because of her condition, they may simply have went straight to eating her alive.
In the Shining Armor Arc, it turns out that Makarov'sAlicorn Cyborgs were all ponies he abducted and forcibly transformed. Now they're trapped in their own twisted bodies, unable to stop themselves from killing at his whim.
Some of the Mane Cast in Sweetie's Mansion is this when they temporarly become Sweetie's Spirit Advisor to help her defeat their ghostly selves whenever she takes a picture of one. Luna on the other hand is well aware that her spirit is under the control of Specter but she can't stop herself from attacking Sweetie Belle, Luna can only warn her what her ghostly self is about to do like the mane cast who became Spirit Advisors for Sweetie.
In Pages Of Harmony, after Twilight Sparkle kills the other Elements of Harmony, they don't move on to the afterlife. Instead, they're trapped in a limbo-like state where they can see and hear Twilight, but she can only hear them. And their Mind Raped personalities are still intact even after they die.
Plenty to go around in The Conversion Bureau: The Other Side of the Spectrum. Due to it being a DeconstructiveHate Fic to the TCB genre (especially the works of Chatoyance), it's a given that ponification is this. The author Redskin 122004, however, went above and beyond in making it horrifying though, and they're frequently referred to as perpetuallysmilingzombies on the tropes page and among the fans. The single crowning moment of Nightmare Fuel for them, however, has to be the fact that the human converts' souls are literally broken to pieces and bound to Queen Celestia and Tirek's will. Even worse, according to the Zebra shaman Quagga, it is utterly impossible to repair said souls; only death will make the newfoals' souls whole again. Meaning even if the Queen and the bag are defeated, only masseuthanasia will set their souls free.
Marcus (describing the potion): "Rewrites a person into a pony... changes their body, their mind, binds their soul in chains... takes them away from you."
The Wham Episode chapter For Whom the Bell Tolls reveals that this is also the case for the TCB Universe's Mane Six. When Canon!Luna fishes around in TCB!Twilight's mind to gather some information, she discovers that Queen Celestia personally Mind Raped each of the girls by imprisoning them in their own minds and then implanting evil new personalities to drive their bodies around to carry out her will. All the TCB!Mane Six could do over the three long years of the war was helplessly watch on as their controlled bodies commit Moral Event Horizon grade acts against the humans and other species of Equis. TCB!Twilight herself is reduced to a horribly broken and sobbing wreck who desperately begs Luna to kill her already and stop the madness.
In the fic Two Moons, Deidara's soul is removed from his body during a fight with Orochimaru, and takes up residence in the back of Itachi's head. Fittingly, Deidara isn't pleased (he actually does scream for quite a bit), and is completely incapable of getting even Itachi to realize he's there. He is also incapable of sleeping, and has to experience every thought and every bit of sensory input that Itachi does. The author admits that writing a chapter sometimes makes her head hurt as much as the readers'.
One can almost pity Madara in A Growing Affection. Hinata's Singularity Rasangan atomizes him, and according to the description seems to slow down time like a real black hole. Due to his immortality being tied to his eyes, he doesn't die until they are consumed. And fittingly, he tries to scream in pain but the sound cannot escape.
It happens to Young Link in Link's New Look: Playing Princess where due to Peach's "special" perfume he was forced to act like a girly princess while he was unable to do anything about it.
A similar fate happens to Ben Tennyson in Ben's New Look: Mallrats where due to Gwen's Feminisa poseon spell he was forced to act like a girly girl in a crowded mall while he can't do anything about it.
It also happened to every boy except ironically Naruto himself in Naruto's New Look due to the caged bird seal used by Shizune.
Song of the Phoenix. The souls of certain victims of Jusenkyo —the ones who originally drowned in the springs to create the curses in the first place— are trapped in the waters. Some of them "sleep" in blissful oblivion... others exist in absolute, endless darkness as nothing but thinking souls, for however many thousands of years it takes for someone to fall in the spring and, if they're exceedingly lucky, hitch a ride in their body. They can only watch from within the body, unable to interact, until the cursed person dies and the other soul is allowed to manifest briefly. And then they go right back into the spring, and the darkness... It is explicitly stated that the soul of the Drowned Girl from the spring that cursed Ranma went through this for 1500 years, to the other characters' horror.
Praying in Vain: Over the course of the story the protagonist finds and frees the victim/s and the murderer/s of several killings throughout the town's history, trapped in its Dark Worldever since they were killed and continually experiencing their moment of death (including but not limited to bleeding to death, dismemberment and immolation). It's heavily implied that every single person killed there is in a similar state, forever tortured to sustain the town's Genius Loci and at the end, though pissed at the loss of its food, the personification of the aforementioned loci assures the protagonist that she has accomplished nothing, and that there is plenty more where they came from.
The fate of anyone who is subject to Forceless possession in Paranormalities. Not only do Forceless completely hijack the host's body and physically shape (read: mutilate) it to their desire, the victim is consciously aware of what is happening to him/her and only those with Force Sensitivity can tell of their predicament. Death is a mercy for those who have been possessed (especially for Dynn Manthis). So far, the only exceptions to this rule are those who willingly serve the Forceless Collective, Maesterus and Zolph Vaelor. Maesterus and Zolph are part of the same bloodline, and the immunity has strengthened every generation. Maesterus was still mutated by the Forceless symbiote, but he eventually became immune to the body-jacking, while Zolph was always immune to possession altogether, thus making him the number one threat to the Collective.
In Part 2 of Clash of the Elements, this is Cackletta's final fate, in which her 'Second Life' spell in combination with Alpha's nanomachines will leave her in a perpetual state of life and death until the spell runs out.
TRONFanon holds that rectification is like this, the poor Program intermittently conscious and aware of the horrible things s/he is doing to serve their "masters," but unable to stop themselves from carrying it out.
Early in a Werewolf: The Apocalypse fan fic, the main character suffers sleep paralysis in his bathtub and wakes up right before drowning. As if that wasn't horrifying enough, the character is later kidnapped by the villains and forcefully possessed by an evil spirit. He likens it to the episode he suffered earlier, except he actually drowns.
In Yu-Gi-Oh The Thousand Year Door, Redux, the Shadow Queen spent the first few three centuries of so of her millennium-long imprisonment like this; she was manacled tightly in a very small, dark cell, unable to move a muscle, fully awake and aware. For much of the fic, the readers - and the protagonists - are led to believe that the Three Heroes mercilessly sentenced her to this fate, and never intended to release her. The truth comes out much later. The same magic that made her a prisoner was supposed to administer therapy to nurture her mind so that hopefully, once all her crimes were forgotten over ten centuries, she could be released after accepting redemption. She was even offered a chance to sleep through it. She rejected both, and fought to free herself of the chains until she succeeded, and then spend centuries plotting revenge.